Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020947.1 Corchorus olitorius cultivar O-4 contig20980, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15037
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Found at i:1028 original size:53 final size:56
Alignment explanation
Indices: 971--1116 Score: 192
Period size: 59 Copynumber: 2.6 Consensus size: 56
961 TTTTAATTAA
* * * *
971 TTCATTTTACTCTTTAGTTTCCGAA-TTTTAC-C-AATTACTC-TTTCATTATCTCT
1 TTCATTTTACTCTTTAATTACC-AAGCTTTACTCTAATTACCCATTTCATTATCTCT
1024 TTCATTTTACTCTTTAATTACCAAGCTTTACTCTTTAATTACCCAATTTCATTATCTCT
1 TTCATTTTACTCTTTAATTACCAAGCTTTACTC--TAATTACCC-ATTTCATTATCTCT
1083 TTCATTTTACTCTTTAATTACCAAGCTTTACTCT
1 TTCATTTTACTCTTTAATTACCAAGCTTTACTCT
1117 TTAATTAGCC
Statistics
Matches: 82, Mismatches: 4, Indels: 10
0.85 0.04 0.10
Matches are distributed among these distances:
52 2 0.02
53 25 0.30
54 1 0.01
57 8 0.10
59 46 0.56
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (56 bp):
TTCATTTTACTCTTTAATTACCAAGCTTTACTCTAATTACCCATTTCATTATCTCT
Found at i:1038 original size:13 final size:13
Alignment explanation
Indices: 1005--1038 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
995 ATTTTACCAA
1005 TTACTCTTTCATT
1 TTACTCTTTCATT
*
1018 AT-CTCTTTCATT
1 TTACTCTTTCATT
1030 TTACTCTTT
1 TTACTCTTT
1039 AATTACCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (13 bp):
TTACTCTTTCATT
Found at i:1093 original size:59 final size:59
Alignment explanation
Indices: 1011--1131 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
1001 CCAATTACTC
1011 TTTCATTATCTCTTTCATTTTACTCTTTAATTACCAAGCTTTACTCTTTAATTACCCAA
1 TTTCATTATCTCTTTCATTTTACTCTTTAATTACCAAGCTTTACTCTTTAATTACCCAA
*
1070 TTTCATTATCTCTTTCATTTTACTCTTTAATTACCAAGCTTTACTCTTTAATTAGCCAA
1 TTTCATTATCTCTTTCATTTTACTCTTTAATTACCAAGCTTTACTCTTTAATTACCCAA
1129 TTT
1 TTT
1132 AATTTTAATT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.50
Consensus pattern (59 bp):
TTTCATTATCTCTTTCATTTTACTCTTTAATTACCAAGCTTTACTCTTTAATTACCCAA
Found at i:1114 original size:21 final size:22
Alignment explanation
Indices: 1088--1128 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1078 TCTCTTTCAT
1088 TTTACTCTTTAATTA-CCAAGC
1 TTTACTCTTTAATTAGCCAAGC
1109 TTTACTCTTTAATTAGCCAA
1 TTTACTCTTTAATTAGCCAA
1129 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (22 bp):
TTTACTCTTTAATTAGCCAAGC
Found at i:1229 original size:40 final size:39
Alignment explanation
Indices: 1151--1268 Score: 106
Period size: 35 Copynumber: 3.1 Consensus size: 39
1141 TTTCATTCTG
* *
1151 ACCAAATTCTTTTTTACTTTACCAAAATTTCTTTTTTATT
1 ACCAAATTCTTTTTTACGTTACC-AAATTCCTTTTTTATT
*
1191 ACCAAATTCTTTTTTA-GTTACC-AATTCCTTTTACT-TT
1 ACCAAATTCTTTTTTACGTTACCAAATTCCTTTT-TTATT
** *
1228 A-TTAATT-TTTTTTA-ATTACCAAATT-CTTTTTTACTT
1 ACCAAATTCTTTTTTACGTTACCAAATTCCTTTTTTA-TT
1264 ACCAA
1 ACCAA
1269 TTTTACTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
34 1 0.02
35 17 0.27
36 11 0.17
37 13 0.20
38 1 0.02
39 5 0.08
40 16 0.25
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (39 bp):
ACCAAATTCTTTTTTACGTTACCAAATTCCTTTTTTATT
Found at i:1270 original size:18 final size:19
Alignment explanation
Indices: 1151--1268 Score: 120
Period size: 18 Copynumber: 6.3 Consensus size: 19
1141 TTTCATTCTG
1151 ACCAAATTCTTTTTTACTTT
1 ACCAAATTCTTTTTTAC-TT
1171 ACCAAAATTTCTTTTTTA-TT
1 ACC-AAA-TTCTTTTTTACTT
*
1191 ACCAAATTCTTTTTTAGTT
1 ACCAAATTCTTTTTTACTT
*
1210 ACC-AATTC-CTTTTACTTT
1 ACCAAATTCTTTTTTAC-TT
** *
1228 A-TTAATT-TTTTTTAATT
1 ACCAAATTCTTTTTTACTT
1245 ACCAAATTCTTTTTTACTT
1 ACCAAATTCTTTTTTACTT
1264 ACCAA
1 ACCAA
1269 TTTTACTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
17 8 0.10
18 31 0.38
19 22 0.27
20 8 0.10
21 3 0.04
22 10 0.12
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (19 bp):
ACCAAATTCTTTTTTACTT
Found at i:1325 original size:32 final size:31
Alignment explanation
Indices: 1289--1447 Score: 149
Period size: 31 Copynumber: 5.3 Consensus size: 31
1279 ACTCTTTTAA
1289 TTACCGAATTCTTTTTAATTCTTTTTAATTAC
1 TTACC-AATTCTTTTTAATTCTTTTTAATTAC
* *
1321 TTACCAATT-TTACTTTTACTC-TTTTAATTAC
1 TTACCAATTCTT--TTTAATTCTTTTTAATTAC
*
1352 ---CAAATTCTTTTTAATTCTTTTTAATTAC
1 TTACCAATTCTTTTTAATTCTTTTTAATTAC
* *
1380 TTACCAATT-TTACTTTTACTC-TTTTAATTAC
1 TTACCAATTCTT--TTTAATTCTTTTTAATTAC
*
1411 ---CAAATTCTTTTTAATTCTTTTTAATTAC
1 TTACCAATTCTTTTTAATTCTTTTTAATTAC
1439 TTACCAATT
1 TTACCAATT
1448 TTACTTTTAC
Statistics
Matches: 101, Mismatches: 12, Indels: 29
0.71 0.08 0.20
Matches are distributed among these distances:
27 12 0.12
28 30 0.30
29 4 0.04
30 4 0.04
31 34 0.34
32 17 0.17
ACGTcount: A:0.27, C:0.17, G:0.01, T:0.55
Consensus pattern (31 bp):
TTACCAATTCTTTTTAATTCTTTTTAATTAC
Found at i:1482 original size:32 final size:32
Alignment explanation
Indices: 1269--1485 Score: 137
Period size: 32 Copynumber: 7.2 Consensus size: 32
1259 TACTTACCAA
*
1269 TTTTACTTTTACTCTTTTAATTACCGAATTCT
1 TTTTACTTTTACTCTTTTAATTACCAAATTCT
* ** * *
1301 TTTTA--ATT-CT-TTTTAATTA-CTTA-CCAA
1 TTTTACTTTTACTCTTTTAATTACCAAATTC-T
1328 TTTTACTTTTACTCTTTTAATTACCAAATTCT
1 TTTTACTTTTACTCTTTTAATTACCAAATTCT
* ** * *
1360 TTTTA--ATT-CT-TTTTAATTA-CTTA-CCAA
1 TTTTACTTTTACTCTTTTAATTACCAAATTC-T
1387 TTTTACTTTTACTCTTTTAATTACCAAATTCT
1 TTTTACTTTTACTCTTTTAATTACCAAATTCT
* ** * *
1419 TTTTA--ATT-CT-TTTTAATTA-CTTA-CCAA
1 TTTTACTTTTACTCTTTTAATTACCAAATTC-T
1446 TTTTACTTTTACTCTTTTAATTACCAAATTCT
1 TTTTACTTTTACTCTTTTAATTACCAAATTCT
1478 TTTTACTT
1 TTTTACTT
1486 ACCAATTTTA
Statistics
Matches: 134, Mismatches: 30, Indels: 42
0.65 0.15 0.20
Matches are distributed among these distances:
26 3 0.02
27 21 0.16
28 27 0.20
29 12 0.09
30 12 0.09
31 27 0.20
32 29 0.22
33 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTTACTTTTACTCTTTTAATTACCAAATTCT
Found at i:1485 original size:45 final size:47
Alignment explanation
Indices: 1439--2177 Score: 586
Period size: 51 Copynumber: 15.2 Consensus size: 47
1429 TTTTAATTAC
* *
1439 TTACCAATTTTACTTTTAC-TCTTTTAATTACCAAA-TTCTTTTTAC
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTTCTTTTTAA
* * *
1484 TTACCAATTTTACTTTTAC-TCTCTTAATTACCAAA-TTCTTTTTAC
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTTCTTTTTAA
* *
1529 TTACCAATTTTACTTTTAC-TCTCTTAATTACCAAATTCTCTTTTTTTTTAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATT-TC----TTTTTAA
* *
1580 TTACCATTTTTACTTTTACTTTTTTTAGTTACCAAATTCTCTTTTTTTTAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATT-TC---TTTTTAA
1631 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTTTTTTAAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATT-TC----TTTTT-AA
*
1684 TTACCAATTTTACTTTTACTTTTTTTAATTACCGAATTCACTTTTTTTTTAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACC-AA---A-TTTCTTTTTAA
1736 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTCTTTTTTTTAAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAA-T-T-TC---TTTTT-AA
* *
1790 TTA-CATATTTTACTTTTACTTTTTTTTACTTACCAAA-TTCTTCTT--
1 TTACCA-ATTTTACTTTTAC-TTTTTTTAATTACCAAATTTCTTTTTAA
**** **** *
1835 TTA-C--TTTT--TTTTAC-TTACCAAATT-CTTTTTTTC-TTCTAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTTCTTTTTAA
*
1874 TTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTCTTTTTTTAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAA-T-TTC--TTTTTAA
* * *
1925 TTACCAATTTTACTTTTACATTTTTTTTACTTACCAAA-TTCTCTTTAC
1 TTACCAATTTTACTTTTAC--TTTTTTTAATTACCAAATTTCTTTTTAA
* * *
1973 TTACCAATTTTACTTTTACTTTTTTTTTACTTACCAAA-TTCTCTTTAC
1 TTACCAATTTTACTTTTAC--TTTTTTTAATTACCAAATTTCTTTTTAA
* * **
2021 TTACCAATTTTACTTTTACTCTTTTTTACTTACCAAATTCTTTTTTTTTTC
1 TTACCAATTTTACTTTTACT-TTTTTTAATTACCAAA---TTTCTTTTTAA
* * *
2072 TTACCAATTTTACTTTTAC-TCTTTTAATTACCAAATTCTTTTTTTTTA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAA-T-TTCTTTTTAA
* *
2120 TTACCAATTTTACTTTTACTTTTTTTTTACTTACCAAA-TTCTTTTT-T
1 TTACCAATTTTACTTTTAC--TTTTTTTAATTACCAAATTTCTTTTTAA
2167 TTACCAATTTT
1 TTACCAATTTT
2178 TTAGATAACC
Statistics
Matches: 598, Mismatches: 48, Indels: 94
0.81 0.06 0.13
Matches are distributed among these distances:
37 3 0.01
38 8 0.01
39 3 0.01
40 7 0.01
42 8 0.01
44 6 0.01
45 88 0.15
46 3 0.01
47 31 0.05
48 115 0.19
49 15 0.03
50 4 0.01
51 141 0.24
52 62 0.10
53 64 0.11
54 20 0.03
55 16 0.03
57 2 0.00
58 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (47 bp):
TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTTCTTTTTAA
Found at i:1629 original size:23 final size:23
Alignment explanation
Indices: 1552--1785 Score: 135
Period size: 28 Copynumber: 9.1 Consensus size: 23
1542 TTTTACTCTC
1552 TTAATTACCAAATTCTCTTTTTTT
1 TTAATTACCAAATTCTC-TTTTTT
** *
1576 TTAATTACCATTTTTACTTTTACTTTTT
1 TTAATTACCA-AATT-C-TCT--TTTTT
*
1604 TTAGTTACCAAATTCTCTTTTTT
1 TTAATTACCAAATTCTCTTTTTT
* *
1627 TTAATTACCAATTTTACTTTTACTTTTT
1 TTAATTACCAA-ATT-C-TCT--TTTTT
1655 TTAATTACCAAATTCTCTTTTTTT
1 TTAATTACCAAATTCTC-TTTTTT
* *
1679 TTAAATTACCAATTTTACTTTTACTTTTT
1 TT-AATTACCAA-ATT-C-TCT--TTTTT
* *
1708 TTAATTACCGAATTCACTTTTTTT
1 TTAATTACCAAATTCTC-TTTTTT
* *
1732 TTAATTACCAATTTTACTTTTACTTTTT
1 TTAATTACCAA-ATT-C-TCT--TTTTT
1760 TTAATTACCAAATTCTCTCTTTTT
1 TTAATTACCAAATTCTCT-TTTTT
1784 TT
1 TT
1786 TAAATTACAT
Statistics
Matches: 163, Mismatches: 24, Indels: 46
0.70 0.10 0.20
Matches are distributed among these distances:
23 15 0.09
24 42 0.26
25 19 0.12
26 14 0.09
27 11 0.07
28 55 0.34
29 7 0.04
ACGTcount: A:0.24, C:0.16, G:0.01, T:0.59
Consensus pattern (23 bp):
TTAATTACCAAATTCTCTTTTTT
Found at i:1676 original size:51 final size:51
Alignment explanation
Indices: 1439--1836 Score: 500
Period size: 45 Copynumber: 7.9 Consensus size: 51
1429 TTTTAATTAC
* *
1439 TTACCAATTTTACTTTTAC-TCTTTTAATTACCAAA-T-TC---TTTTTAC
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTTTTTAA
* * *
1484 TTACCAATTTTACTTTTAC-TCTCTTAATTACCAAA-T-TC---TTTTTAC
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTTTTTAA
* *
1529 TTACCAATTTTACTTTTAC-TCTCTTAATTACCAAATTCTCTTTTTTTTTAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTC-TTTTTTTTAA
* *
1580 TTACCATTTTTACTTTTACTTTTTTTAGTTACCAAATTCTCTTTTTTTTAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTTTTTAA
1631 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTTTTTTAAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTC-TTTTTTTT-AA
* *
1684 TTACCAATTTTACTTTTACTTTTTTTAATTACCGAATTCACTTTTTTTTTAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTC-TTTTTTTTAA
1736 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTCTTTTTTTTAAA
1 TTACCAATTTTACTTTTACTTTTTTTAATTACCAAA-T-TCTCTTTTTTTT-AA
*
1790 TTA-CATATTTTACTTTTACTTTTTTTTACTTACCAAATTCTTCTTTT
1 TTACCA-ATTTTACTTTTAC-TTTTTTTAATTACCAAATTC-TCTTTT
1837 ACTTTTTTTT
Statistics
Matches: 325, Mismatches: 13, Indels: 21
0.91 0.04 0.06
Matches are distributed among these distances:
45 79 0.24
46 1 0.00
47 2 0.01
51 73 0.22
52 63 0.19
53 63 0.19
54 28 0.09
55 16 0.05
ACGTcount: A:0.25, C:0.18, G:0.01, T:0.57
Consensus pattern (51 bp):
TTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTTTTTAA
Found at i:1678 original size:53 final size:52
Alignment explanation
Indices: 1234--1836 Score: 581
Period size: 59 Copynumber: 11.5 Consensus size: 52
1224 CTTTATTAAT
*
1234 TTTTTTTAATTACCAAA-T-TC---TTTTTTACTTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTCTCTTTTTTTTTAATTACCAATTTTACTTTTAC
* * *
1281 -TCTTTTAATTACCGAATTCTTTTTAATTCTTTTTAATTACTTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTC-TCTT--TT-TTTTT-A--A-TTACCAATTTTACTTTTAC
* *
1340 -TCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAATTACTTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTC-TCTT--TT-TTTTT-A--A-TTACCAATTTTACTTTTAC
* *
1399 -TCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAATTACTTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTC-TCTT--TT-TTTTT-A--A-TTACCAATTTTACTTTTAC
* *
1458 -TCTTTTAATTACCAAA-T-TC----TTTTTACTTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTCTCTTTTTTTTTAATTACCAATTTTACTTTTAC
* * *
1503 -TCTCTTAATTACCAAA-T-TC----TTTTTACTTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTCTCTTTTTTTTTAATTACCAATTTTACTTTTAC
* * *
1548 -TCTCTTAATTACCAAATTCTCTTTTTTTTTAATTACCATTTTTACTTTTAC
1 TTTTTTTAATTACCAAATTCTCTTTTTTTTTAATTACCAATTTTACTTTTAC
*
1599 TTTTTTTAGTTACCAAATTCTC-TTTTTTTTAATTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTCTCTTTTTTTTTAATTACCAATTTTACTTTTAC
1650 TTTTTTTAATTACCAAATTCTCTTTTTTTTTAAATTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTCTCTTTTTTTTT-AATTACCAATTTTACTTTTAC
* *
1703 TTTTTTTAATTACCGAATTCACTTTTTTTTTAATTACCAATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTCTCTTTTTTTTTAATTACCAATTTTACTTTTAC
1755 TTTTTTTAATTACCAAATTCTCTCTTTTTTTTAAATTA-CATATTTTACTTTTAC
1 TTTTTTTAATTACCAAATTCTCT-TTTTTTTT-AATTACCA-ATTTTACTTTTAC
*
1809 TTTTTTTTACTTACCAAATTCTTCTTTT
1 -TTTTTTTAATTACCAAATTC-TCTTTT
1837 ACTTTTTTTT
Statistics
Matches: 509, Mismatches: 20, Indels: 46
0.89 0.03 0.08
Matches are distributed among these distances:
45 79 0.16
46 15 0.03
47 3 0.01
48 1 0.00
49 6 0.01
51 73 0.14
52 68 0.13
53 60 0.12
54 19 0.04
55 27 0.05
56 5 0.01
58 1 0.00
59 152 0.30
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.57
Consensus pattern (52 bp):
TTTTTTTAATTACCAAATTCTCTTTTTTTTTAATTACCAATTTTACTTTTAC
Found at i:1823 original size:83 final size:81
Alignment explanation
Indices: 1570--1931 Score: 325
Period size: 78 Copynumber: 4.5 Consensus size: 81
1560 CAAATTCTCT
* * * *
1570 TTTTTTTTAATTACCATTTTTACTTTTACTTTTTTTAGTTACCAAATTCTCTTTTT-TT-TAATT
1 TTTTTTTTACTTACCAATTTT-CTTTTACTTTTTTTAATTACCAAATTCTTTTTTTCTTCTAATT
1633 ACCAATTTTACTTTTAC
65 ACCAATTTTACTTTTAC
* * * * *
1650 -TTTTTTTAATTACCAA-ATTCTCTTT--TTTTTTAAATTACCAATTTTACTTTTACTTT-TTTT
1 TTTTTTTTACTTACCAATTTTCT-TTTACTTTTTTTAATTACCAA-ATT-CTTTT--TTTCTTCT
*
1710 AATTACCGAA-TTCAC---T--
61 AATTACC-AATTTTACTTTTAC
*
1726 TTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTCTTTTT-TT-TAA
1 TTTTTTTTACTTACCAATTTT-CTTTTACTTTTTTTAATTACCAAATTCT-T-TTTTTCTTCT-A
1789 ATTA-CATATTTTACTTTTAC
62 ATTACCA-ATTTTACTTTTAC
*
1809 TTTTTTTTACTTACCAAATTCTTCTTTTACTTTTTTTTACTTACCAAATTCTTTTTTTCTTCTAA
1 TTTTTTTTACTTACC-AATT-TTCTTTTAC-TTTTTTTAATTACCAAATTCTTTTTTTCTTCTAA
1874 TTACCAATTTTACTTTTAC
63 TTACCAATTTTACTTTTAC
*
1893 -TTTTTTTACTTACCAA-ATTC--TT-CTTTTTTTAATTACCAA
1 TTTTTTTTACTTACCAATTTTCTTTTACTTTTTTTAATTACCAA
1932 TTTTACTTTT
Statistics
Matches: 239, Mismatches: 15, Indels: 60
0.76 0.05 0.19
Matches are distributed among these distances:
76 30 0.13
77 24 0.10
78 33 0.14
79 20 0.08
80 25 0.10
81 13 0.05
82 4 0.02
83 33 0.14
84 32 0.13
85 25 0.10
ACGTcount: A:0.24, C:0.16, G:0.01, T:0.59
Consensus pattern (81 bp):
TTTTTTTTACTTACCAATTTTCTTTTACTTTTTTTAATTACCAAATTCTTTTTTTCTTCTAATTA
CCAATTTTACTTTTAC
Found at i:1865 original size:156 final size:151
Alignment explanation
Indices: 1234--1836 Score: 471
Period size: 156 Copynumber: 3.9 Consensus size: 151
1224 CTTTATTAAT
* *
1234 TTTTTTTAATTACCAAATT--C---TTTTTTACTTACCAATTTTACTTTTAC-TCTTTTAATTAC
1 TTTTTTTAATTACCAAATTCACTTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTAC
* * *
1293 CGAATTCTTTTTAATTCTTTTTAATTACTTACCAATTTTACTTTTAC-TCTTTTAATTACCAAAT
66 CAAATTC--TCT--TT-TTTTT-A--A-TTACCAATTTTACTTTTACTTTTTTTAATTACCAAAT
*
1357 TCTTTTTAATTCTTTTTAATTACTTACCAAT-TTTAC
122 TC-TCTT--TT-TTTTTAA--A-TTACCAATATTTAC
* *
1393 TTTTACTCTTTTAATTACCAAATTCTTTTTAATTCTTTTTAATTACTTACCAATTTTACTTTTAC
1 --TT--T-TTTTAATTACCAAATTC-----ACTT-TTTTT--TTAATTACCAATTTTACTTTTAC
* * * *
1458 -TCTTTTAATTACCAAA-T-TC---TTTTTACTTACCAATTTTACTTTTAC-TCTCTTAATTACC
53 TTTTTTTAATTACCAAATTCTCTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTACC
*
1516 AAA-T-TC----TTTTT-ACTTACCAAT-TTTAC
118 AAATTCTCTTTTTTTTTAAATTACCAATATTTAC
* *
1542 TTTTACTCTCTTAATTACCAAATTCTCTTTTTTTTTAATTACCATTTTTACTTTTACTTTTTTTA
1 -TTT--T-T-TTAATTACCAAATTCACTTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTA
*
1607 GTTACCAAATTCTCTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTC
61 ATTACCAAATTCTCTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTC
1672 TTTTTTTTTAAATTACCAATTTTACTTTTAC
126 TTTTTTTTTAAATTACCAA---TA--TTTAC
*
1703 TTTTTTTAATTACCGAATTCACTTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTAC
1 TTTTTTTAATTACCAAATTCACTTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTAC
*
1768 CAAATTCTCTCTTTTTTTTAAATTA-CATATTTTACTTTTACTTTTTTTTACTTACCAAATTCTT
66 CAAA-T-TCTCTTTTTTTT-AATTACCA-ATTTTACTTTTAC-TTTTTTTAATTACCAAATTC-T
1832 CTTTT
125 CTTTT
1837 ACTTTTTTTT
Statistics
Matches: 375, Mismatches: 22, Indels: 90
0.77 0.05 0.18
Matches are distributed among these distances:
141 21 0.06
142 14 0.04
143 6 0.02
144 4 0.01
146 1 0.00
147 27 0.07
148 18 0.05
149 29 0.08
150 2 0.01
152 1 0.00
153 5 0.01
154 5 0.01
155 8 0.02
156 60 0.16
157 2 0.01
158 16 0.04
159 18 0.05
160 23 0.06
161 13 0.03
162 1 0.00
163 35 0.09
164 16 0.04
166 1 0.00
167 5 0.01
173 1 0.00
175 4 0.01
176 1 0.00
177 38 0.10
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.57
Consensus pattern (151 bp):
TTTTTTTAATTACCAAATTCACTTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTAC
CAAATTCTCTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTAATTACCAAATTCTCTTTTT
TTTTAAATTACCAATATTTAC
Found at i:1887 original size:48 final size:49
Alignment explanation
Indices: 1810--2175 Score: 268
Period size: 48 Copynumber: 7.3 Consensus size: 49
1800 TACTTTTACT
***
1810 TTTTTTTACTTACCAAATTCTTCTTTTAC-TTTTTTTTACTTACCAAATTC
1 TTTTTTT-CTTACC-AATTCCAATTTTACTTTTTTTTTACTTACCAAATTC
*
1860 TTTTTTTCTT-CTAATTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTC
1 TTTTTTTCTTACCAATT-CCAATTTTAC--TT--TTTTTTTACTTACCAAA---TTC
* ** * *
1916 TTTTTTTAATTACCAATTTTACTTTTACATTTTTTTTACTTACCAAATTC
1 TTTTTTT-CTTACCAATTCCAATTTTACTTTTTTTTTACTTACCAAATTC
* * ** *
1966 -TCTTTACTTACCAATTTTACTTTTACTTTTTTTTTACTTACCAAATTC
1 TTTTTTTCTTACCAATTCCAATTTTACTTTTTTTTTACTTACCAAATTC
* * ** * *
2014 -TCTTTACTTACCAATTTTACTTTTAC-TCTTTTTTACTTACCAAATTC
1 TTTTTTTCTTACCAATTCCAATTTTACTTTTTTTTTACTTACCAAATTC
* *
2061 TTTTTTT-TT-TC--TTACCAATTTTACTTTTACTCTTTTAATTACCAAATTC
1 TTTTTTTCTTACCAATT-CCAATTTTACTTTT--T-TTTTACTTACCAAATTC
* ** *
2110 TTTTTTTTTATTACCAATTTTACTTTTACTTTTTTTTTACTTACCAAATTC
1 --TTTTTTTCTTACCAATTCCAATTTTACTTTTTTTTTACTTACCAAATTC
2161 -TTTTTT-TTACCAATT
1 TTTTTTTCTTACCAATT
2176 TTTTAGATAA
Statistics
Matches: 265, Mismatches: 28, Indels: 49
0.77 0.08 0.14
Matches are distributed among these distances:
44 2 0.01
45 7 0.03
46 3 0.01
47 35 0.13
48 85 0.32
49 23 0.09
50 10 0.04
51 24 0.09
52 3 0.01
53 35 0.13
54 11 0.04
55 3 0.01
56 10 0.04
57 9 0.03
58 5 0.02
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (49 bp):
TTTTTTTCTTACCAATTCCAATTTTACTTTTTTTTTACTTACCAAATTC
Found at i:1922 original size:23 final size:23
Alignment explanation
Indices: 1840--1931 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 23
1830 TTCTTTTACT
* *
1840 TTTTTTTACTTACCAAATTCTTT
1 TTTTTTTAATTACCAAATTCTTC
*
1863 TTTTCTTCTAATTACCAATTTTACTTTTAC
1 TTTT-TT-TAATTACCAA-ATT-C--TT-C
*
1893 TTTTTTTACTTACCAAATTCTTC
1 TTTTTTTAATTACCAAATTCTTC
1916 TTTTTTTAATTACCAA
1 TTTTTTTAATTACCAA
1932 TTTTACTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
23 20 0.36
24 4 0.07
25 9 0.16
26 3 0.05
27 3 0.05
28 9 0.16
29 4 0.07
30 4 0.07
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTTTAATTACCAAATTCTTC
Found at i:1987 original size:147 final size:140
Alignment explanation
Indices: 1832--2177 Score: 392
Period size: 147 Copynumber: 2.3 Consensus size: 140
1822 CCAAATTCTT
1832 CTTTTACTTTTTTTTACTTACCAAATTCTTTTTTTCTTCTAATTACCAATTTTACTTTTACT-TT
1 CTTTTACTTTTTTTTACTTACCAAATTC------TCTT-TAATTACCAATTTTACTTTTACTCTT
* *
1896 TTTTACTTACCAAATTCTTCTTTTTTTAATTACCAATTTTACTTTTACATTTTTTTTACTTACCA
59 TTTTACTTACCAAATTCTT-TTTTTTTAATTACCAATTTTACTTTTAC---TCTTTTAATTACCA
1961 AATTC-TCTTTACTTACCAATTTTA
120 AATTCTTCTTTA-TTACCAA---TA
*
1985 CTTTTACTTTTTTTTTACTTACCAAATTCTCTTTACTTACCAATTTTACTTTTACTCTTTTTTAC
1 CTTTTAC-TTTTTTTTACTTACCAAATTCTCTTTAATTACCAATTTTACTTTTACTCTTTTTTAC
**
2050 TTACCAAATTCTTTTTTTTTTCTTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTTTT
65 TTACCAAATTCTTTTTTTTTAATTACCAATTTTACTTTTACTCTTTTAATTACCAAATTC---TT
*
2115 TTTTATTACCAATTTTA
127 CTTTATTACCAA---TA
**
2132 CTTTTACTTTTTTTTTACTTACCAAATTCT-TTTTTTTACCAATTTT
1 CTTTTAC-TTTTTTTTACTTACCAAATTCTCTTTAATTACCAATTTT
2178 TTAGATAACC
Statistics
Matches: 179, Mismatches: 8, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
144 17 0.09
146 14 0.08
147 90 0.50
148 30 0.17
153 7 0.04
154 21 0.12
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.59
Consensus pattern (140 bp):
CTTTTACTTTTTTTTACTTACCAAATTCTCTTTAATTACCAATTTTACTTTTACTCTTTTTTACT
TACCAAATTCTTTTTTTTTAATTACCAATTTTACTTTTACTCTTTTAATTACCAAATTCTTCTTT
ATTACCAATA
Found at i:1991 original size:99 final size:99
Alignment explanation
Indices: 1810--2177 Score: 436
Period size: 99 Copynumber: 3.7 Consensus size: 99
1800 TACTTTTACT
* *
1810 TTTTTTTACTTACCAAATTCTT-CTTTTACTTTTTTTTACTTACCAAATTCTTTTTTTCTTCTAA
1 TTTTTTTAATTACC-AATT-TTACTTTTACTTTTTTTTACTTACCAAATTC-----TTCTT-TAC
1874 TTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTC
58 TTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTC
1916 TTTTTTTAATTACCAATTTTACTTTTACATTTTTTTTACTTACCAAATTC-TCTTTACTTACCAA
1 TTTTTTTAATTACCAATTTTACTTTTAC-TTTTTTTTACTTACCAAATTCTTCTTTACTTACCAA
1980 TTTTACTTTTACTTTTTTTTTACTTACCAAATTC-TC
65 TTTTACTTTTAC--TTTTTTTACTTACCAAATTCTTC
* * * *
2016 ----TTTACTTACCAATTTTACTTTTACTCTTTTTTACTTACCAAATTCTTTTTTTTTTCTTACC
1 TTTTTTTAATTACCAATTTTACTTTTACTTTTTTTTACTTACCAAATTC---TTCTTTACTTACC
* *
2077 AATTTTACTTTTAC-TCTTTTAATTACCAAATTCTT-
63 AATTTTACTTTTACTTTTTTTACTTACCAAATTCTTC
*
2112 TTTTTTT-ATTACCAATTTTACTTTTACTTTTTTTTTACTTACCAAATTCTT-TTT-TTTACCAA
1 TTTTTTTAATTACCAATTTTACTTTTAC-TTTTTTTTACTTACCAAATTCTTCTTTACTTACCAA
2174 TTTT
65 TTTT
2178 TTAGATAACC
Statistics
Matches: 237, Mismatches: 11, Indels: 39
0.83 0.04 0.14
Matches are distributed among these distances:
95 31 0.13
96 43 0.18
97 3 0.01
99 64 0.27
100 29 0.12
101 20 0.08
104 2 0.01
105 11 0.05
106 34 0.14
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.59
Consensus pattern (99 bp):
TTTTTTTAATTACCAATTTTACTTTTACTTTTTTTTACTTACCAAATTCTTCTTTACTTACCAAT
TTTACTTTTACTTTTTTTACTTACCAAATTCTTC
Found at i:2036 original size:18 final size:17
Alignment explanation
Indices: 1944--2036 Score: 72
Period size: 18 Copynumber: 5.5 Consensus size: 17
1934 TTACTTTTAC
*
1944 ATTTTTTTTACTTACCAA
1 ATTTTCTTTACTTACC-A
*
1962 ATTCTCTTTACTTACCA
1 ATTTTCTTTACTTACCA
1979 ATTTTACTTTTACTT----
1 ATTTT-C-TTTACTTACCA
1994 -TTTT-TTTACTTACCAA
1 ATTTTCTTTACTTACC-A
*
2010 ATTCTCTTTACTTACCA
1 ATTTTCTTTACTTACCA
2027 ATTTTACTTT
1 ATTTT-CTTT
2037 TACTCTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
11 7 0.12
14 4 0.07
17 13 0.22
18 29 0.48
19 7 0.12
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTCTTTACTTACCA
Found at i:2068 original size:21 final size:22
Alignment explanation
Indices: 2042--2168 Score: 103
Period size: 22 Copynumber: 5.2 Consensus size: 22
2032 ACTTTTACTC
2042 TTTTTTACTTACCAAATTCTTT
1 TTTTTTACTTACCAAATTCTTT
* *
2064 TTTTTTTCTTACCAATTTTACTTT
1 TTTTTTACTTACCAA-ATT-CTTT
*
2088 TACTCTTTTAATTACCAAATTCTTT
1 T--T-TTTTACTTACCAAATTCTTT
2113 TTTTTTA-TTACCAATTTTACTTTTACTTT
1 TTTTTTACTTACCAA----A---TT-CTTT
2142 TTTTTTACTTACCAAATTCTTT
1 TTTTTTACTTACCAAATTCTTT
2164 TTTTT
1 TTTTT
2169 ACCAATTTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 28
0.72 0.04 0.24
Matches are distributed among these distances:
21 7 0.08
22 28 0.33
23 5 0.06
24 5 0.06
25 6 0.07
26 4 0.05
27 11 0.13
28 2 0.02
29 11 0.13
30 7 0.08
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTTACTTACCAAATTCTTT
Found at i:2165 original size:29 final size:28
Alignment explanation
Indices: 2109--2166 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
2099 TTACCAAATT
*
2109 CTTTTTTTTTATTACCAATTTTACTTTTA
1 CTTTTTTTTTATTACCAATTCTA-TTTTA
*
2138 CTTTTTTTTTACTTACCAAATTCTTTTTT
1 CTTTTTTTTTA-TTACC-AATTCTATTTT
2167 TTACCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.44
30 9 0.36
31 5 0.20
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.66
Consensus pattern (28 bp):
CTTTTTTTTTATTACCAATTCTATTTTA
Found at i:10972 original size:1 final size:1
Alignment explanation
Indices: 10966--10991 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
10956 AAAATCAAGG
10966 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
10992 TCCATTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13678 original size:68 final size:68
Alignment explanation
Indices: 13597--14107 Score: 641
Period size: 68 Copynumber: 7.6 Consensus size: 68
13587 CCATCAAAAC
* * *
13597 ATTTCCAAAAATACCCTTTCGGTCGATGGGTCATTTTCGTCTTTTTGCATTTGAGTTTAGTGTTT
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTGTTT
13662 TTT
66 TTT
* *
13665 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTCTTTGCATTTAAGTTTAGTGTTT
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTGTTT
*
13730 TCT
66 TTT
* * *
13733 ATTTCCAAAAATACCCCTTCAGTTGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTGTTT
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTGTTT
*
13798 TCT
66 TTT
*
13801 ATTTCCAAAAATACCCTTTCAGTCGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTG-TT
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTGTTT
13865 TTT
66 TTT
*
13868 ATTTCCAAAAATACCCTTTCGATCGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTGTTT
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTGTTT
13933 TCTT
66 T-TT
* * *
13937 -TTTCCAAAAATACCCTTTCGGTCGAAGGGTAAATTTCAACTTTTT-CATATCTAAG-TTA--GT
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTTGCAT-T-TAAGTTTAGTGT
*
13997 TTTCT
64 TTTTT
* * * * * * * *
14002 -TTTCCCAAAATACTCTTTCGGTCAAAGGGTCA-ATTCTGTCGTTCTTGCATTTGAGTTT--T-C
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTC-ATC-TTTTTGCATTTAAGTTTAGTGT
*
14062 TTTTG
64 TTTTT
* *
14067 ATTTCCAAAACTACCCTTTCGGT-GAAAGGGTCAGTTTCATC
1 ATTTCCAAAAATACCCTTTCGGTCG-AAGGGTCATTTTCATC
14108 ACTTCCGCAT
Statistics
Matches: 394, Mismatches: 37, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
64 3 0.01
65 36 0.09
66 41 0.10
67 73 0.19
68 235 0.60
69 6 0.02
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (68 bp):
ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTTGCATTTAAGTTTAGTGTTT
TTT
Done.